Hi Rodolfo,
> On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> > On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo <raram...@tamu.edu> wrote:
> >> Dave,
> >>
> >> It did contain errors as reported by tailing the last part of the
> >> INSTALLATION.log
> >>
> >> Thanks
> >>
> >> --Rodolfo
> >
> > Looks like your BOOST is too new for BLAST 2.2.26+ (which
> > just recently became a problem on the Galaxy Tool Shed testing
> > system as well).
> >
> > In the short term I'm hoping to update the Tool Shed repository
> > to use the NCBI provided pre-compiled binaries. I'm in discussion
> > with Galaxy's Dave Bouvier about how best to do that, perhaps
> > with some relatively new functionality added to Galaxy. Next,
> > updating the BLAST+ version (and the unit tests to match).
> >
> > I would suggest right now you manually install BLAST+ using
> > the NCBI provided binaries.
> >
> > Peter
>
> Boost is a funny thing
> Changes a lot
> A package compiled with one Boost version might fail to compile with a
> newer one. I have seen it a lot
> You either have to download Boost and link to the specific version you
> want before compiling your package or provide pre-compiled binaries
> The question I have is: How many Galaxy packages have Boos as a
> dependency for compilation? and if the answer is: a lot, then would it
> be smart for Galaxy to have a place where it can keep versions of
> these commonly-used libraries so that they can be linked by packages
> that need to be compiled 'in-situ' or would it be just more efficient
> to provide pre-compiled binaries?
> Something tells me that pre-compiled binaries might not take full
> advantage of the hardware they are and that compiling is better...
> So, should ToolShed installation require automatic download of a set
> of pre-defined commonly-used libraries?

As Peter already mentioned, the plan is to link specific versions of a
tool to one specific version of boost. boost will also be installed and
compiled. We plan to have a orphan tool dependency for every boost
version like that one:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53
To see how it should work, please have a look at my RDKit repository:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/rdkit
Regarding your concerns about performance limitations with pre-compiled
binaries, you are probably right. But do not forget the installation and
compilation happens on one cluster node and the other nodes may also be
different. So even with compiled versions you are not guaranteed to take
full advantages of your hardware.
Cheers,
Bjoern
>
> --Rodolfo
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/